Awns reduce grain number to increase grain size and harvestable yield in irrigated and rainfed spring wheat.

Genotypic variation in ear morphology is linked to differences in photosynthetic potential to influence grain yield in winter cereals. Awns contribute to photosynthesis, particularly under water-limited conditions when canopy assimilation is restricted. We assessed performance of up to 45 backcross-derived, awned-awnletted NILs representing four diverse genetic backgrounds in 25 irrigated or rainfed, and droughted environments in Australia and Mexico. Mean environment grain yields were wide-ranging (1.38-7.93 t ha(-1)) with vegetative and maturity biomass, plant height, anthesis date, spike number, and harvest index all similar (P >0.05) for awned and awnletted NILs. Overall, grain yields of awned-awnletted sister-NILs were equivalent, irrespective of yield potential and genetic background. Awnletted wheats produced significantly more grains per unit area (+4%) and per spike (+5%) reflecting more fertile spikelets and grains in tertiary florets. Increases in grain number were compensated for by significant reductions in grain size (-5%) and increased frequency (+0.8%) of small, shrivelled grains ('screenings') to reduce seed-lot quality of awnletted NILs. Post-anthesis canopies of awnletted NILs were marginally warmer over all environments (+0.27 °C) but were not different and were sometimes cooler than awned NILs at cooler air temperatures. Awns develop early and represented up to 40% of total spikelet biomass prior to ear emergence. We hypothesize that the allocation of assimilate to large and rapidly developing awns decreases spikelet number and floret fertility to reduce grain number, particularly in distal florets. Individual grain size is increased to reduce screenings and to increase test weight and milling quality, particularly in droughted environments. Despite the average reduction in grain size, awnless lines could be identified that combined higher grain yield with larger grain size, increased grain protein concentration, and reduced screenings.

Genomic-enabled prediction with classification algorithms.

Pearson's correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait-environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen's kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets) and the best RE in the same 13 data sets, with values ranging from 0.393 to 0.948 (statistically significant in 12 data sets). RR produced the best mean for both κ and RE in one data set (0.148 and 0.381, respectively). Regarding the wheat data sets, SVC-lin presented the best κ in 12 of the 16 data sets, with outcomes ranging from 0.280 to 0.580 (statistically significant in 4 data sets) and the best RE in 9 data sets ranging from 0.484 to 0.821 (statistically significant in 5 data sets). SVC-rbf (0.235), RR (0.265) and RHKS (0.422) gave the best κ in one data set each, while RHKS and BL tied for the last one (0.234). Finally, BL presented the best RE in two data sets (0.738 and 0.750), RFR (0.636) and SVC-rbf (0.617) in one and RHKS in the remaining three (0.502, 0.458 and 0.586). The difference between the performance of SVC-lin and that of the rest of the models was not so pronounced at higher percentiles of the distribution. The behaviour of regression and classification algorithms varied markedly when selection was done at different thresholds, that is, κ and RE for each algorithm depended strongly on the selection percentile. Based on the results, we propose classification method as a promising alternative for GS in plant breeding.

Genomic prediction in CIMMYT maize and wheat breeding programs.

Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required.

Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example.

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.

A paradigm shift towards low-nitrifying production systems: the role of biological nitrification inhibition (BNI).

BACKGROUND: Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems. SCOPE: In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed 'biological nitrification inhibition' (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4(+))-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and environmental perspective, the BNI function in plants could potentially have a large influence on biogeochemical cycling and closure of the N loop in crop-livestock systems.

A QTL on chromosome 6A in bread wheat (Triticum aestivum) is associated with longer coleoptiles, greater seedling vigour and final plant height.

Wheat crops with greater early vigour shade the soil surface more rapidly and reduce water loss. Evaporative losses affect water-use efficiency particularly in drier regions where most of the rainfall occurs early in the growing season before canopy closure. Greater seedling leaf area and longer coleoptiles are major determinants of increased vigour and better crop establishment. A previously developed high vigour breeding line 'Vigour 18' was used to establish a large recombinant inbred family and framework map to identify a QTL on chromosome 6A that accounted for up to 8% of the variation for coleoptile length, 14% of seedling leaf width and was associated with increased plant height. The SSR marker NW3106, nearest to the 6A QTL, was also associated with greater leaf width in a breeding population that was also derived from a cross involving the high vigour donor line 'Vigour18'. The association between the NW3106 marker and coleoptile length was validated in a second breeding population which was developed using an unrelated long coleoptile donor line. The 'Vigour18' allele of the QTL on chromosome 6A promoted coleoptile length and leaf width during early plant growth but was also associated with increased plant height at maturity. Markers linked to the QTL are being used to increase the frequency of increased vigour and long coleoptile alleles in early generations of breeding populations.

Molecular mapping of genes for Coleoptile growth in bread wheat (Triticum aestivum L.).

Successful plant establishment is critical to the development of high-yielding crops. Short coleoptiles can reduce seedling emergence particularly when seed is sown deep as occurs when moisture necessary for germination is deep in the subsoil. Detailed molecular maps for a range of wheat doubled-haploid populations (Cranbrook/Halberd, Sunco/Tasman, CD87/Katepwa and Kukri/Janz) were used to identify genomic regions affecting coleoptile characteristics length, cross-sectional area and degree of spiralling across contrasting soil temperatures. Genotypic variation was large and distributions of genotype means were approximately normal with evidence for transgressive segregation. Narrow-sense heritabilities were high for coleoptile length and cross-sectional area indicating a strong genetic basis for differences among progeny. In contrast, heritabilities for coleoptile spiralling were small. Molecular marker analyses identified a number of significant quantitative trait loci (QTL) for coleoptile growth. Many of the coleoptile growth QTL mapped directly to the Rht-B1 or Rht-D1 dwarfing gene loci conferring reduced cell size through insensitivity to endogenous gibberellins. Other QTL for coleoptile growth were identified throughout the genome. Epistatic interactions were small or non-existent, and there was little evidence for any QTL x temperature interaction. Gene effects at significant QTL were approximately one-half to one-quarter the size of effects at the Rht-B1 and Rht-D1 regions. However, selection at these QTL could together alter coleoptile length by up to 50 mm. In addition to Rht-B1b and Rht-D1b, genomic regions on chromosomes 2B, 2D, 4A, 5D and 6B were repeatable across two or more populations suggesting their potential value for use in breeding and marker-aided selection for greater coleoptile length and improved establishment.

A local diagnostic reference level for velopharyngeal investigations.

The purpose of this study was to derive an initial local diagnostic reference level for velopharyngeal investigations carried out as standard radiological practice in the Medical Imaging Department, Queen Victoria Hospital, East Grinstead. This is a specialist video-fluoroscopic radiological technique used to evaluate velopharyngeal dysfunction, especially for paediatric patients. A retrospective analysis over a period of 7 months involving 50 examinations yielded dose-area product values ranging from 0.04 Gy cm(2) (minimum) to 0.37 Gy cm(2) (maximum) with a mean value of 0.11 Gy cm(2) and 3rd quartile value of 0.12 Gy cm(2). The maximum effective dose was estimated as 0.016 mGy. An initial local diagnostic reference level of 0.12 Gy cm(2) has been levied.

A design study for a 'spiral staircase' ionization chamber for the quality control of electron beams.

In order to verify that the energies of electron beams used for external beam therapy remain constant, IPEM 81 recommends a constancy check based on the ratio of ionization chamber measurements at two depths along the central axis. Such measurements for a range of electron energies can be a time consuming process. The purpose of this study was to design a device that would use several ion chambers simultaneously to measure electron depth dose curves, and hence the electron energy. A design was developed for a device consisting of ten independent ionization chambers, shaped and arranged in a solid phantom like the steps of a spiral staircase, the axis of the staircase being coincident with the axis of the electron beam. Measurements were carried out to test the design of individual chambers and to optimize the radius of the spiral and both the depth intervals and the lateral spacing between adjacent chambers. For ranges of electron energy from 6-12 MeV and 12-20 MeV the radii of the spirals needed were found to be 36.5 mm and 30.9 mm, the angular separations between edges of the chambers were 52 degrees and 30 degrees and chamber depths were found to be 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 mm and 20, 40, 45, 50, 55, 60, 65, 70, 75, 80 mm, respectively.

A comparison of polyacrylamide gels and radiochromic film for source measurements in intravascular brachytherapy.

For intravascular brachytherapy with catheter-based systems, AAPM Task Group 60 has recommended measurements that should be made to characterize the sources. Beta emitters, including (90)Sr/(90)Y are ideal for intravascular brachytherapy, but problems arise in measuring dose distributions in the high dose gradient region at short distances from the source. In this paper, measurements of radial and orthogonal dose distributions and dose profiles for a (90)Sr/(90)Y source train using polyacrylamide gel (PAG) dosimetry and a high-field 4.7 Tesla MRI scanner are presented and compared with measurements made with two types of radiochromic film, MD-55 and HD-810. For the PAG system, the dose distributions were determined with in-plane resolutions of 0.4 mm and 0.2 mm. The measurements of absorbed dose distributions both orthogonal and parallel to the source axis show good agreement between the PAG and radiochromic film. The absolute dose at a radial distance of 2 mm in the central 32 mm of a line parallel to the axis was measured. For the PAG the measured absorbed dose was 1.25% lower, for MD-55 4% higher and for the HD-810 1.6% higher when compared with the value given by the source calibration. These results confirm that both absorbed dose and dose distributions for high gradient vascular brachytherapy sources can be measured using PAG but the disadvantages of gel manufacture and the need for access to a high resolution scanner suggests that the use of radiochromic film is the method of choice.

Recording accelerator monitor units during electronic portal imaging: application to collimator position verification during IMRT.

The application of multiple portal image acquisition to collimator position verification during dynamic multileaf collimation (DMLC) using a commercial camera-based electronic portal imaging device (EPID) (Theraview, Cablon Medical BV, Leusden, The Netherlands) mounted on an Elekta SL15i accelerator (Elekta Oncology Systems, Crawley, UK) is described. This is achieved using a custom-built dose acquisition system optically interfaced to both the camera control unit of the EPID and the monitor unit (MU) channel of the accelerator. The method uses the beam blanking camera control signal to trigger the dose acquisition system to read the cumulative accelerator MUs at the beginning and end of each period of image formation. A maximum delay of 15 ms has been estimated for recording of accelerator MUs in the current system. The camera interface was observed to have no effect on the operation of the EPID during normal clinical use and could therefore be left permanently in situ. Use of the system for collimator position verification of a test case is presented. The technique described uses a specific camera-based EPID and accelerator, although the general principle of using an EPID control signal to trigger recording of accelerator MUs may be applicable to other EPIDs/accelerators with suitable knowledge of the accelerator dosimetry system.

Measurement of the response of Gd2O2S:Tb phosphor to 6 MV x-rays.

The phosphor GdO2S:Tb is widely used in camera-based electronic portal imaging devices (EPIDs). There is considerable interest in the application of EPIDs to dosimetry and the verification of intensity modulated radiation therapy produced by dynamic multileaf collimation (DMLC). This paper presents direct measurement of Gd2O2S:Tb phosphor luminescence under 6 MV x-ray irradiation from a linear accelerator using a photomultiplier tube. The luminescence following each radiation pulse (3 micros duration) was observed to decay with a dominant lifetime of 558 micros. Using a specialized electrometer, the temporal variation of the optical signal has been compared with the dose rate incident on the phosphor measured using a semiconductor diode detector. Under dose rates typical of those used in the clinic (1.2 Gy min(-1) to the phosphor), measurements at beam-start confirmed that the optical signal is linear with dose per radiation pulse. Measurements at beam termination following phosphor doses up to 4.4 Gy showed no residual signal associated with long-lived luminescence (afterglow) from the phosphor above the noise level of the optical signal (0.17% standard deviation). This measurement demonstrates that afterglow from Gd2O2S:Tb is not of significance for its application to DMLC verification. Additionally, it was confirmed that the accelerator pulse repetition frequency has no effect on the optical signal from the phosphor in the range 25-400 Hz.

A method for controlling image acquisition in electronic portal imaging devices.

Certain types of camera-based electronic portal imaging devices (EPIDs) which initiate image acquisition based on sensing a change in video level have been observed to trigger unreliably at the beginning of dynamic multileaf collimation sequences. A simple, novel means of controlling image acquisition with an Elekta linear accelerator (Elekta Oncology Systems, Crawley, UK) is proposed which is based on illumination of a photodetector (ORP-12, Silonex Inc., Plattsburgh, NY, USA) by the electron gun of the accelerator. By incorporating a simple trigger circuit it is possible to derive a beam on/off status signal which changes at least 100 ms before any dose is measured by the accelerator. The status signal does not return to the beam-off state until all dose has been delivered and is suitable for accelerator pulse repetition frequencies of 50-400 Hz. The status signal is thus a reliable means of indicating the initiation and termination of radiation exposure, and thus controlling image acquisition of such EPIDs for this application.

Dosimetric properties of the Theraview fluoroscopic electronic portal imaging device.

Electronic portal imaging devices (EPIDs) can be used for non-imaging applications in radiotherapy such as patient dosimetry. Of the systems available, the fluoroscopic camera-based EPID Theraview (InfiMed Inc.) has not been studied to date, and a review of the dosimetric properties of the system is presented here. In the "single set-up" mode of image acquisition, pixel intensity increases sublinearly with applied dose. The response was dependent on the system's video signal gain and showed a threshold dose to the detector in the range 0.05-0.35 cGy, and pixel saturation at detector doses in the range 1.2-1.6 cGy. Repeated exposures of the EPID were observed to be extremely reproducible (standard deviation 0.5%). The sensitivity of the system showed a linear decline of 0.04% day-1 over a 68-day period, during which time the relative off-axis response within 10 x 10 cm2 field was constant to within a standard deviation of 0.56%. The system shows spatial non-uniformity, which requires correction for application to dose measurements in two-dimensions. Warm-up of the camera control unit required a period of at least 40 min and was associated with an enhancement in pixel intensity of up to 12%. A radiation dose history effect was observed at doses as low as 0.2 Gy. Camera dark current was shown to be negligible at normal accelerator operation. No discernible image distortion was found. Mechanical stability on gantry rotation was also assessed and image displacement of up to 5 mm at the isocentre was observed. It was concluded that the device could be used for dosimetry provided necessary precautions were observed and corrections made.

The potential use of polymer gel dosimetry in boron neutron capture therapy.

Polymer gels with and without 60 ppm of 10B were exposed to an epithermal neutron beam produced by the Dynamitron at the University of Birmingham on two separate occasions. Eight vials containing the gel, four with and four without boron, were irradiated in pairs in a water phantom for 5 h. The maximum dose was calculated to be 9 Gy in A-150 tissue equivalent plastic, 4 cm deep in the phantom. Measurements were made of the variation of relaxation rates of the gels with depth in a phantom. These were compared with calculations using the MCNP Monte Carlo program and the gel response followed the general trend of the results of the calculations. The calculations showed that the absence of boron gave 66.1% and 44.3% of the absorbed dose with boron and the measurements showed the response of the gel without boron to give 65+/-2% and 41+/-6% of the response with boron for the two halves of the first vial. All the gel measurements showed an enhancement in absorbed dose when boron was added. These results indicate that polymer gels may have a role in measuring the enhancement of absorbed dose due to boron in an epithermal or thermal neutron.

An investigation into the use of polymer gel dosimetry in low dose rate brachytherapy.

An investigation has been carried out into the properties of the BANG polymer gel and its use in the dosimetry of low dose rate brachytherapy. It was discovered that the response of the gel was reproducible and linear to 10 Gy. The gel was found to be tissue equivalent with a response independent of energy to within experimental accuracy (standard error of measurement +/- 5%). The slope of the calibration curve was found to increase from 0.28 +/- 0.01 s-1 Gy-1 to 0.50 +/- 0.02 s-1 Gy-1 for an increase in monomer concentration from 6 to 9%. Absorbed dose distributions for a straight applicator containing 36 137Cs sources were measured using the gel and the results compared with measurements made with thermoluminescent dosemeters (TLDs) and calculated values. Good agreement was found for the relative measurements. The root mean square residual percentage errors were 3%, 1% and 4% for the gel and the two groups of TLDs, respectively. There were some significant differences in absolute values of absorbed dose in the gel, possibly owing to the effects of oxygen. Measurements of a complex gynaecological insert were also made and compared with isodose curves from a planning system (Helax TMS), and in areas unaffected by oxygen diffusion the isodose levels from 100 to 50% agreed to within less than 0.5 mm.

An evaluation of the potential and limitations of three-dimensional reconstructions from intravascular ultrasound images.

Three-dimensional (3D) reconstructions of arteries can be produced using two-dimensional (2D) intravascular ultrasound (IVUS) images. Any artefact that affects 2D images has the potential to limit the quality of a 3D reconstruction. Using a catheter withdrawal technique, a range of test rigs were used to assess: (i) the effect of rotation of the probe orientation; (ii) the ability to reconstruct the true path of a tortuous vessel; (iii) the effect of image distortion on diameter measurements; (iv) the number of images per unit length used to produce a 3D reconstruction; and (v) the quality of the IVUS 3D reconstruction of a stent. These investigations show that 3D IVUS imaging is prone to artefacts. For 3D IVUS images to be used to quantify the vessel path or to make accurate measurements of vessel dimensions, more information about the catheter tip position and orientation is required than is currently available with the pullback technique.

Supplement to the code of practice for clinical proton dosimetry. ECHED (European Clinical Heavy Particle Dosimetry Group).

The 'Code of Practice for Clinical Proton Dosimetry' (Vynckier, S., Bonnett, D.E. and Jones, D.T.L. Code of practice for clinical proton dosimetry. Radiother. Oncol. 20: 53-63, 1991) was published in 1991, but since then new data for mass stopping powers have been reported and consideration has been given to the specification of absorbed dose in water instead of the original recommendation of absorbed dose in tissue. This supplement summarises the basic recommendations of the original Code of Practice and incorporates the new stopping power data for dose specification in water.

The development of an interdepartmental audit as part of a physics quality assurance programme for external beam therapy.

A cost-effective audit system has been developed that will both detect systematic error in data and procedures and evaluate the quality assurance programme provided by a physics department for radiotherapy. The audit has been developed for external beam radiotherapy and assesses one modality and one treatment machine per year. The audit is carried out on an interdepartmental basis and can be undertaken by two physicists from each department in one working day. The method of assessing the quality assurance programme and the schedule of measurements are described. The process is illustrated using the results of trial audits between the medical physics departments at Coventry and Leicester.

Current developments in proton therapy: a review.

The use of high-energy protons in radiotherapy was first proposed in 1946. In the last decade there has been a significant growth in the number of centres using protons in the treatment of malignant and non-malignant disease. To date (January 1993) a total of more than 11,500 patients have been treated world-wide. Encouraging clinical results have been reported in the literature. The purpose of this article is to outline the advantages of proton beams and to review current developments in physics and engineering applied to the field of proton therapy with particular emphasis on proton accelerator technology and the development of proton therapy facilities. The production of clinically useful beams is discussed and the relative merits of different treatment systems compared. Reference is also made to the factors affecting the absorbed dose in a patient and to proton radiobiology together with the results of studies of comparisons of treatment planning with protons with that using conventional photon therapy. The dosimetry of proton beams is also reviewed.